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pcamasigpro [2010/03/12 16:52]
mjnueda
pcamasigpro [2014/05/12 12:42]
jcarbonell
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 __Parameters for //​PCA-maSigFun gene selection//​__:​ __Parameters for //​PCA-maSigFun gene selection//​__:​
    ​*//​Data//:​ txt file with expression data, genes in rows, arrays in columns. The file must contain an additional row with arrays names and a column with gene names.\\    ​*//​Data//:​ txt file with expression data, genes in rows, arrays in columns. The file must contain an additional row with arrays names and a column with gene names.\\
 +\\
 +|Name|Array1|Array2|Array3|Array4|Array5|Array6|Array7|Array8|Array9|…|
 +|gene1|0.5|0.2|0.7|1.3|1.4|1.0|2.1|2.4|2.6|…|
 +|gene2|0.5|0.3|0.4|0.3|0.4|0.1|0.1|0.4|0.5|…|
 +|...|...|...|...|...|...|...|...|...|...|…|
 +\\
    ​*//​Covariates//:​ txt file with experimental design information,​ containing as many columns as arrays and as many rows as experimental factor. Each cell contains the value of the array in the experimental factor. E.g:    ​*//​Covariates//:​ txt file with experimental design information,​ containing as many columns as arrays and as many rows as experimental factor. Each cell contains the value of the array in the experimental factor. E.g:
 \\ \\
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 by applying several procedures: by applying several procedures:
    ​*//​Resampling//:​ where a null Leverage distribution is created by permuting columns of expression data and genes are selected at the "​alpha"​ percentile of the null distribution.    ​*//​Resampling//:​ where a null Leverage distribution is created by permuting columns of expression data and genes are selected at the "​alpha"​ percentile of the null distribution.
-   ​*//​minAS//:​ where a density function is calculated on the data and genes are selected on a local minimum basis. +   ​*//​minAS//:​ where a density function is calculated on the data and genes are selected on a local minimum basis [[references |[7]]]
-   ​*//​Gamma//:​ where a gamma distribution is adjusted to the distributions of the gene loadings, and genes are selected at the "​alpha"​ percentile of the gamma distribution. ​+   ​*//​Gamma//:​ where a gamma distribution is adjusted to the distributions of the gene loadings, and genes are selected at the "​alpha"​ percentile of the gamma distribution ​[[references |[7]]]
    ​*//​Custom//:​ where the user can decide the threshold.    ​*//​Custom//:​ where the user can decide the threshold.
 \\ \\
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pcamasigpro.txt · Last modified: 2014/05/12 12:42 by jcarbonell
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